context("Processing of residue series")
# FOCUS (2014) page 76 (parent) and page 132 (metabolite)
parent_1 <- c(.12, .09, .05, .03, "nd", "nd", "nd", "nd", "nd", "nd")
parent_2 <- c(.12, .09, .05, .03, "nd", "nd", .03, "nd", "nd", "nd")
parent_3 <- c(.12, .09, .05, .03, "nd", "nd", .06, "nd", "nd", "nd")
metabolite <- c("nd", "nd", "nd", 0.03, 0.06, 0.10, 0.11, 0.10, 0.09, 0.05, 0.03, "nd", "nd")
test_that("Simple residue series are processed as intended", {
expect_equal(set_nd_nq(parent_1, 0.02),
c(.12, .09, .05, .03, .01, rep(NA, 5)))
expect_equal(set_nd_nq(parent_2, 0.02, loq = 0.05),
c(.12, .09, .05, .03, .01, .01, .03, .01, NA, NA))
expect_equal(set_nd_nq(metabolite, 0.02, loq = 0.05),
c(NA, NA, .01, .03, .06, .1, .11, .1, .09, .05, .03, .01, NA))
expect_equal(set_nd_nq(c("nd", 1, 0.2, "nd"), 0.1),
c(NA, 1, 0.2, 0.05))
})
test_that("Simple residue series are processed as in the FOCUS guidance", {
# Parent 1
expect_error(set_nd_nq_focus(parent_1, 0.02),
"You need to specify an LOQ")
expect_equal(set_nd_nq_focus(parent_1, 0.02, 0.05),
c(.12, .09, .05, .03, .01, rep(NA, 5)))
# Parent 2
expect_equal(set_nd_nq_focus(parent_2, 0.02, loq = 0.05),
c(.12, .09, .05, .03, .01, rep(NA, 5)))
# Parent 3
expect_equal(set_nd_nq_focus(parent_3, 0.02, loq = 0.05),
c(.12, .09, .05, .03, .01, .01, .06, .01, NA, NA))
# Metabolite
expect_equal(set_nd_nq_focus(metabolite, 0.02, loq = 0.05),
c(0, NA, .01, .03, .06, .1, .11, .1, .09, .05, .03, .01, NA))
})
test_that("Examples Boesten et al. (2015, p. 57/58) are correctly processed", {
table_8 <- matrix(
c(10, 10, rep("nd", 4),
10, 10, rep("nq", 2), rep("nd", 2),
10, 10, 10, "nq", "nd", "nd",
"nq", 10, "nq", rep("nd", 3),
"nd", "nq", "nq", rep("nd", 3),
rep("nd", 6), rep("nd", 6)),
ncol = 6, byrow = TRUE)
table_8_processed <- set_nd_nq(table_8, 0.5, 1.5, time_zero_presence = TRUE)
table_9 <- matrix(
c(10, 10, 0.25, 0.25, NA, NA,
10, 10, 1, 1, 0.25, NA,
10, 10, 10, 1, 0.25, NA,
1, 10, 1, 0.25, NA, NA,
0.25, 1, 1, 0.25, NA, NA,
NA, 0.25, 0.25, NA, NA, NA,
rep(NA, 6)),
ncol = 6, byrow = TRUE)
expect_equal(table_8_processed, table_9)
table_10 <- matrix(
c(10, 10, rep("nd", 4),
10, 10, rep("nd", 4),
10, 10, 10, rep("nd", 3),
"nd", 10, rep("nd", 4),
rep("nd", 18)),
ncol = 6, byrow = TRUE)
table_10_processed <- set_nd_nq(table_10, 0.5, time_zero_presence = TRUE)
table_11 <- matrix(
c(10, 10, 0.25, rep(NA, 3),
10, 10, 0.25, rep(NA, 3),
10, 10, 10, 0.25, NA, NA,
0.25, 10, 0.25, rep(NA, 3),
NA, 0.25, rep(NA, 4),
rep(NA, 12)),
ncol = 6, byrow = TRUE)
expect_equal(table_10_processed, table_11)
})